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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors: Tim Moore
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import numpy as np
import pytest
import mdtraj as md
from mdtraj.geometry import shape
from mdtraj.testing import eq
"""The trajectories `2lines.pdb` and `3lines.pdb` contain several frames of,
respectively, 2 and 3 "residues" each consisting of two atoms in different
orientations relative to one another.
`2lines.pdb`
Frame 0: || in x - S2 should be 1.0
Frame 1: || in y - S2 should be 1.0
Frame 2: || in z - S2 should be 1.0
Frame 3: |- in x/y - S2 should be 0.25
Frame 4: |- in y/z - S2 should be 0.25
`3lines.pdb`
Frame 0: ||| in x - S2 should be 1.0
Frame 1: ||| in y - S2 should be 1.0
Frame 2: ||| in z - S2 should be 1.0
Frame 3: at right angles - S2 should be 0.0
"""
@pytest.fixture()
def traj1(get_fn):
return md.load(get_fn("1line.pdb"))
@pytest.fixture()
def traj2(get_fn):
return md.load(get_fn("2lines.pdb"))
@pytest.fixture()
def traj3(get_fn):
return md.load(get_fn("3lines.pdb"))
@pytest.fixture()
def traj4(get_fn):
return md.load(get_fn("2koc.pdb"))
def test_gyration(traj1, traj2, traj3):
assert eq(
shape.compute_gyration_tensor(traj1),
shape._compute_gyration_tensor_slow(traj1),
)
assert eq(
shape.compute_gyration_tensor(traj2),
shape._compute_gyration_tensor_slow(traj2),
)
assert eq(
shape.compute_gyration_tensor(traj3),
shape._compute_gyration_tensor_slow(traj3),
)
def test_principal_moments(traj4):
rg_actual = md.compute_rg(traj4)
principal_moments = shape.principal_moments(traj4)
rg_computed = np.sqrt(principal_moments.sum(axis=1))
assert eq(rg_actual, rg_computed)
def test_asphericity(traj4):
b_computed = shape.asphericity(traj4)
pm = shape.principal_moments(traj4)
rg = md.compute_rg(traj4)
b_actual = 1.5 * pm[:, 2] - rg**2 / 2.0
assert eq(b_actual, b_computed)
def test_shape_metrics(traj4):
b = shape.asphericity(traj4)
c = shape.acylindricity(traj4)
rg = md.compute_rg(traj4)
kappa_actual = (b**2 + 0.75 * c**2) / (rg**4)
kappa_computed = shape.relative_shape_anisotropy(traj4)
assert eq(kappa_actual, kappa_computed)
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